My clever colleague Stu found this blog post which solved our problem with the ECB menu and arrow down link (on our custom master page), which was positioned incorrectly and so making it impossible for users to open...
By default, SharePoint use the style class .s4-ctx to control the menu position, It uses inline “absolute” positioning to show the correct Icon “position: absolute” so add the following code in your custom css:
/* fix scrolling on list pages */
#s4-bodyContainer
{
position:relative;
}